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I've got the same problem, I'm running a debian linux 3.0 with emacs 21.1, 
however, this solution can work on every linux distribution...

You must add the following lines to your .xintrc or .xsession file in your 
home user directory:

    xmodmap -e "keycode 115 = Super_L"
    xmodmap -e "keycode 116 = Super_L"
    xmodmap -e "add mod4 = Super_L"

read the xmodmap doc for details...